The difference between merge and integration with Seurat objects
I have two questions:
When can we use merge for Seurat objects? When can we use integration for Seurat objects?
I have two datasets from different experiments. each dataset has cancer samples and healthy samples. To do clustering, I did the following:
1- I created a Seurat object for each sample, then I calculated QC and filtered the cell.
2- normalized each object with SCT
3- combined samples from each experiment together using merge() and then I made a list of two objects (two experiments)
4- applied reference-based integration to combine the two datasets. I used two samples (cancer and health) with high cell number from each dataset as a reference dataset.
4- Run PCA, UMAP, Find Neighbour, FindCluster.
This workflow worked, however, I am unsure if what I have done correctly in biology?
For one dataset with many samples, Could I apply the Seurat integration workflow instead of merge()?
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